Following the Enterprise's return to the 23rd century they were contacted by Starfleet Control, and were informed by Kirk that the Enterprise was home. (TOS: "Tomorrow is Yesterday")

Based on the single reference of this agency, and referenced at a time when the Enterprise appeared to operate under several agencies ("command base", "Starfleet Command", "Spacefleet Command", "United Earth Space Probe Agency"), it is unclear if Starfleet Control was intended to be an alternate name for Starfleet Command, or if it was an agency within Starfleet that maintained the responsibilities similar to modern day mission controls.